Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.
Every file beside index.md is one the mold kind declares.
target-specific fields are coherent.
Abstract oracle: the properties any cast of this Mold must satisfy.
eval.md declares properties and check type.
eval.md ↗Concrete cases bound to fixtures, run against the eval properties.
scenarios.md declares cases bound to fixtures.
scenarios.md ↗12 typed references; 0 resolver issues.
All on-demand references describe triggers.
Hypothesis references include verification.
Typed references describe what casting consumes, and when the generated skill should load each artifact.
Structured contract copied for validation or lookup.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Structured contract copied for validation or lookup.
Structured contract copied for validation or lookup.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Same draft with one additional step concretized (one loop iteration). Once every step is concrete, [[draft-next-step]] reports `draft: false` and the harness exits the loop.
Concrete gxformat2 workflow (`class: GalaxyWorkflow`) extracted from the fully-concretized draft at loop endstate via [[draft-extract]]: drafty steps dropped, `_plan_*` planning fields stripped, class promoted. The runnable, testable artifact that downstream Molds ([[implement-galaxy-workflow-test]], [[validate-galaxy-workflow]], [[run-workflow-test]]) consume.
Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.
gxformat2 draft (see [[galaxy-workflow-draft-format]]) mutated in-place across iterations; topology is fully concrete, individual tool steps may still carry `TODO_*` sentinels and `_plan_*` planning fields.
Carried obligations ledger [[open-requirements-ledger]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.
Orchestrator Mold for the per-step Galaxy authoring loop. One invocation advances the gxformat2 draft by one step: pick → resolve a wrapper → summarize the wrapper → implement the step → validate. The harness loop reduces to while (gxwf draft-next-step <wf>).draft: invoke skill.
This Mold is single-entry, single-exit: it owns the loop oracle (draft-next-step) and the per-step validator (draft-validate --concrete). Iterations terminate when the draft has no remaining drafty steps; the call that leaves no drafty step (or a call that finds none) extracts the concrete galaxy-workflow.gxwf.yml (via draft-extract) — that promoted-class workflow, not the -draft file, is what downstream Molds test and run — and the harness then drops out of the loop and proceeds to terminal validation via validate-galaxy-workflow.
Choose a writable tool-cache directory for the run. Pass the same --cache-dir <dir> to cache commands, wrapper summarization, and validation.
Pick. Run draft-next-step. If draft: false, the loop is done: apply step 5 to any open blocking entry, then run draft-extract to emit the concrete galaxy-workflow.gxwf.yml (drafty steps dropped, _plan_* stripped, class promoted to GalaxyWorkflow), then return. Otherwise carry the chosen step id forward. If an open blocking entry against it already records the wrapper as confirmed absent, the author branch as ruled out, or why its wired inputs can’t supply the step, go to step 5. Tool Shed misses and a tool version missing from a cache don’t record that.
Resolve a wrapper. First check for an existing pin:
tool_id named by the chosen step’s _plan_* context or identity pin. Reuse its tool_id and tool_version, skipping discover-shed-tool for Tool Shed wrappers or cache/version lookup for stock tools. An embedded user-defined tool has no tool_id: match a sibling whose run: carries the authored definition the plan calls for, by its id and version, and reuse that definition instead of authoring it again. Continue to step 3.Otherwise, split on whether the step’s tool is a built-in / stock Galaxy tool — a bare id with no owner/repo path (Filter1, sort1, Cut1, Show beginning1, collection ops, __APPLY_RULES__):
Built-in / stock — the bare id is the wrapper identity; it does not route through discover-shed-tool (Tool Shed search) or author-galaxy-tool-wrapper. Only its concrete version needs resolving: the shed serves stock tools by bare id, but its TRS version-list endpoint can’t auto-resolve the version, so read it from a populated cache via galaxy-tool-cache list or take a known pin from the step plan — never hand-guess a stock version. summarize-galaxy-tool then performs the bare-id add/summarize with that explicit --tool-version.
Tool Shed wrapper — branch on whether the template already pinned wrapper identity (see the tiers in galaxy-workflow-draft-format):
tool_id is concrete and tool_version is TODO. Treat the pin as a strong seed: confirm it via discover-shed-tool and resolve the changeset, correcting the tool_id only if discovery contradicts the pin (a pinned id is high-confidence template evidence, not a guess to re-derive from scratch).tool_id is TODO. Search fresh: run discover-shed-tool against the step’s _plan_* context.Either way, if no acceptable shed candidate emerges, fall through to author-galaxy-tool-wrapper.
If the resolved pin is absent from the cache, run add <tool_id> --tool-version <v> --cache-dir <dir> before summarization. In @galaxy-tool-util/cli 1.10.0, validation also fetches and caches missing metadata unless --offline is set; offline validation requires a populated cache.
Summarize the wrapper. If step 2 reused a sibling’s pin, reuse that pin’s galaxy-tool-summary: use the file an earlier iteration wrote, or regenerate it from the cache with galaxy-tool-cache summarize <tool_id> --tool-version <v> --cache-dir <dir> --output <file>. If step 2 fell through to author-galaxy-tool-wrapper or reused an embedded definition, skip summarization: the authored galaxy-user-tool.yml is not in any toolbox or cache, and its own inputs and outputs are the port contract. Otherwise, invoke summarize-galaxy-tool to produce the summary.
Implement. Invoke implement-galaxy-tool-step with the summary, or the authored galaxy-user-tool.yml, and the draft. It resolves the chosen step’s remaining TODO_* / _plan_* slots into a concrete tool_id (confirming or correcting any pinned identity), tool_version, state, and wrapper-determined port names. For an authored tool it embeds the definition under the step’s run: instead, as galaxy-user-tool-workflow-binding describes.
Check the ledger. Inspect the open-requirements-ledger for an open blocking entry against this step: one that implement-galaxy-tool-step appended, or one an earlier call or Mold raised. Once no drafty step is left, any open blocking entry counts, including one on a realized step or with no step. draft-validate cannot catch a computability gap: the connection graph knows ports connect, not what they carry, so the draft validates green even though the step can’t run. If such an entry is present, escalate to repair-galaxy-draft-topology for a bounded structural edit, then update the ledger’s topology_repair budget as the ledger note directs — each repair must leave fewer open blocking entries than it found, under a hard cap, and surrender rather than retry once the cap is reached. Then run draft-next-step: if it reports draft: false, the repair removed the last drafty step, so continue at step 6, which validates and extracts. Otherwise return — the next iteration resumes the loop, realizing any draft-tier steps the repair inserted. With no such entry, continue to validation.
Validate. Run draft-validate <draft> --concrete --strict-state --json --cache-dir <dir>. --strict-state makes skipped tool-state checks fail validation; draft structure and topology checks still run. If metadata is unavailable, resolve the cache or fetch error and retry. On exit 0, run draft-next-step again: if it now reports draft: false, no drafty step is left, so apply step 5 to any open blocking entry, then run draft-extract to emit galaxy-workflow.gxwf.yml before returning, because a while draft harness never invokes the skill again. Route other failures using the JSON diagnostics and the rules below.
draft-validate --concrete --strict-state --json failures, after resolving metadata availability, fall into three buckets:
state) — re-enter implement-galaxy-tool-step with the diagnostic._plan_* contract — wrong datatype, missing parameter, incompatible collection shape) — back out to step 2 and pick a different wrapper, either via discover-shed-tool with refined criteria or by escalating to author-galaxy-tool-wrapper.These are red-draft-validate buckets. The fourth escalation path — a step output uncomputable from its wired inputs — is not one of them: the draft validates green there, so it is detected from the ledger in step 5 above, not from a validation failure.
Consult galaxy-tool-job-failure-reference when the wrapper has explicit failure semantics that affect routing — strict-shell behavior, dynamic outputs, or non-default stdio rules can present as wrapper-choice mismatches even when the static shape validates.
Prior pipelines expressed the iteration as four entries: a discover-or-author branch plus summarize-galaxy-tool, implement-galaxy-tool-step, and validate-galaxy-step. Collapsing them into one orchestrator keeps the per-iteration narrative — including the discover-or-author branch and the failure-routing rules — in a single procedural surface that the cast skill can render coherently. Leaf Molds stay independently castable for ad-hoc invocation; only the pipeline shape changes.